[What I'm trying to learn is a bit long for a single question; so I'm just asking for period sources. I don't believe there's a rule against it; but it doesn't appear common. (I couldn't find an 'internet librarian' or 'research help' subreddit).]
Trying to get a feel for BOTH what people believed scientifically in the Medieval Era and the rituals of those practicing what they believed was Magick.
Particularly looking for areas where scientific knowledge was very wrong; salamanders born of fire, mice born from discarded clothing, etc. Sources I can easily get online would be easier than rarer items from libraries.
As I'm looking for what people believed in the era; sources that are older; but were still widely believed like the works of Pliny the Elder are also helpful.
Specific topics of interest; animals/plants (bestiaries), medicine (apothecary), alchemy, demonology (including Grimoires like the Key of Solomon).
There are hundreds if not thousands of texts that qualify for your description.
I'm going to recommend you look at two key secondary works of review in which you'll find listed and described most chief primary sources. The first is Richard Kieckhefer's Magic in the Middle Ages (Cambridge, 1989, 2000, 2014). Kieckhefer is the foremost historian of magic and witchcraft in the middle ages. He provides a thorough guide to the materials you are asking about, in particular he has organized the 'Further Reading' section by topic. Note that only some of this material exists in English translation.
On books of magic specifically, you should consult Owen Davies' Grimoires: A History of Magic Books (Oxford, 2009). This will give you a quick deep dive into the textual sources to determine what you might want to study in detail.
Beyond the above, you really should look at the following as well:
Lynn Thorndike's The Place of Magic in the Intellectual History of Europe and his 8 volume History of Magic and Experimental Science are older and harder to find but are still key starting points for scholars looking to discern magic from science. The 8 volume set is broken into vol 1-2 < 1300 CE ; vol 3-4 1300-1500 CE ; vol 5-6 1500-1600 CE ; vol 7-8 1600-1700 CE and in them he lists primary sources.
Stuart Clark's Thinking With Demons (Oxford, 1999) is considered to be the most rigorous look at how demonology worked its way into various spheres of early modern intellectual life from culture to law to science with a lot of citations of source materials. There are few people who have ever read as much source material of this subject and in this era than Clark: his primary source list alone is over 50 pages.
Once you've determined the sources you want you can try Archive.org , Project Gutenberg and Google Books to see if they've been scanned up to the web.
Some medieval latin and vernacular texts were translated into English the 19th century and can be found scanned and free. If you know German and French your free 19th c translations will open up greatly.
Hello! Wow, what a broad question.
I've done an AMA on parts of your question (and many others): http://www.reddit.com/r/AskHistorians/wiki/profiles/bemonk
Specifically why alchemists believe what they did. In fact I do a whole podcast on that: http://historyofalchemy.com
Where I go into alchemy, astrology, hermeticism, neoplatonism, kabbalah, etc, etc, etc in a history of science podcast. So why people did experiments the way they did with their expected results. Some alchemy was magic, some astrology, etc. Sources are endless. I highly recommend John Dee if you want to learn about someone who was born in a very superstitious one filled with magic and speaking to angels, and died in a radically more scientific and modern one (though still Early Modern)
Feel free to ask (hopefully narrower) follow up questions.